Date of Award

8-2023

Document Type

Dissertation

Degree Name

Ph.D.

Organizational Unit

College of Natural Science and Mathematics, Chemistry and Biochemistry

First Advisor

Scott Horowitz

Second Advisor

Daniel Linseman

Third Advisor

Michelle Knowles

Fourth Advisor

Sunil Kumar

Fifth Advisor

Martin Margittai

Keywords

Chaperone, G-quadruplex, Nucleic acids, Protein aggregation

Abstract

Understanding the interplay between nucleic acids and protein aggregation is integral to the understanding of proteostasis, aging, and neurodegenerative disease progression. Nucleic acids are known to modulate the aggregation of PrP, tau, ⍺-synuclein, and other disease relevant proteins. Although the interactions between misfolded protein and nucleic acids can play a role in disease, this interaction may potentially be beneficial as well. Our group and others have shown nucleic acids can be powerful chaperones. Previous work has shown both RNA and DNA can prevent protein aggregation and RNA can pass off protein clients to the heat shock protein (Hsp) system. Here we explore the underlying physical properties and kinetics of how nucleic acids prevent protein aggregation. We found that the concentration of bulk dsDNA can be tuned to roughly control the size of kinetically stable protein oligomers. DNA facilitates this oligomerization via the formation of “networks” to rapidly assimilate misfolded proteins to yield smaller oligomers at higher DNA concentrations or larger aggregates at lower DNA concentrations. In a follow up study, we found that G-quadruplexes were an even more powerful chaperone than bulk DNA (which on a per-weight basis was more powerful than any known protein-based chaperone). G-quadruplexes appear to be particularly adept at interacting with misfolded proteins and are also thought to play a role in a number of diseases related to protein aggregation. To find the source of G-quadruplex’s chaperoning ability, we systematically mutated two G-quadruplex forming sequences with solved structures. The solved structures allowed us to make structure function hypotheses, where we found several factors contributed to their remarkable chaperone activity. In particular: their structural topology, overall dynamics and G-quadruplex accessibility, and oligomerization state. Together, this work explores the structural, physical, and mechanistic features of nucleic acids that make them such adept chaperones.

Copyright Date

8-2023

Copyright Statement / License for Reuse

All Rights Reserved
All Rights Reserved.

Publication Statement

Copyright is held by the author. User is responsible for all copyright compliance.

Rights Holder

Theodore J. Litberg

Provenance

Received from ProQuest

File Format

application/pdf

Language

English (eng)

Extent

172 pgs

File Size

18.0 MB

Discipline

Biochemistry, Biophysics, Biology

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